MolNFT v1 · #78514 · protein

Cu-mediated dimer of T4 lysozyme D61H/K65H by synthetic symmetrization

3SB8: “Cu-mediated dimer of T4 lysozyme D61H/K65H by synthetic symmetrization”. X-ray diffraction, 1 ligand (CU), 4 pockets (best druggability 0.82). MolNFT v1 #78514 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3SB8
Type: protein
Length: 492 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysozyme
EC: 3.2.1.17
UniProt: P00720
Ligands: CU
Pockets: 4 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 62% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysozyme (EC 3.2.1.17)	protein	165	61% helix, 9% strand	P00720
B	Lysozyme (EC 3.2.1.17)	protein	164	63% helix, 9% strand	P00720
C	Lysozyme (EC 3.2.1.17)	protein	163	63% helix, 9% strand	P00720

Ligands and binding sites

CU · Copper (II) ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	244	0.82	0.94	34	empty
2	976	0.80	0.82	95	empty
3	162	0.54	0.80	25	empty
4	231	0.53	0.76	31	empty

Interfaces

3 interfaces between chains.

A–B · 833 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 489 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 338 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3SB8 · Cu-mediated Dimer of T4 Lysozyme D61H/K65H by Synthetic Symmetrization · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P00720
Elsewhere: RCSB PDB 3SB8 · PDBe 3SB8 · UniProt P00720

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